Effects of different compost amendments on the abundance and composition of alkB harboring bacterial communities in a soil under industrial use contaminated with hydrocarbons

Abstract

Alkane degrading microorganisms play an important role for the bioremediation of petrogenic contaminated environments. In this study, we investigated the effects of compost addition on the abundance and diversity of bacteria harboring the alkane monooxygenase gene (alkB) in an oil-contaminated soil originated from an industrial zone in Celje, Slovenia (Technosol). Soil without any amendments (control soil) and soil amended with two composts differing in their maturation stage and nutrient availability, were incubated under controlled conditions in a microcosm experiment and sampled after 0, 6, 12, and 36 weeks of incubation. As expected the addition of compost stimulated the degradation of alkanes in the investigated soil shortly after the addition. By using quantitative real-time PCR higher number of alkB genes were detected in soil samples amended with compost compared to the control soils. To get an insight into the composition of alkB harboring microbial communities, we performed next generation sequencing of amplicons of alkB gene fragment. Richness and diversity of alkB gene harboring prokaryotes was higher in soil mixed with compost compared to control soils with stronger effects of the less maturated, nutrient poor compost. The phylogenetic analysis of communities suggested that the addition of compost stimulated the abundance of alkB harboring Actinobacteria during the experiment independent from the maturation stage of the compost. AlkB harboring γ-proteobacteria like Shewanella or Hydrocarboniphaga as well as α-proteobacteria of the genus Agrobacterium responded also positively to the addition of compost to soil. The amendment of the less maturated, nutrient poor compost resulted in addition in a large increase of alkB harboring bacteria of the Cytophaga group (Microscilla) mainly at the early sampling time points. Our data indicates that compost amendments significantly change abundance and diversity pattern of alkB harboring microbes in Technosol and might be a useful agent to stimulate bioremediation of hydrocarbons in contaminated soils.

The ecological and physiological responses of the microbial community from a semiarid soil to hydrocarbon contamination and its bioremediation using compost amendment

“…This issue is even more noticeable in our semiarid soils that contain very low nutrient content [4]. Overall, our results are in agreement with the bio-stimulation capacities of organic amendments for promoting hydrocarbon biodegradation [1,8,9,43]. Furthermore, Plaza et al (2009) [44] indicated that changes in humic acids during composting of organic matter may be expected to facilitate microbial accessibility to PAHs and may result in an effective clean-up.…”

“…compost, sludges) has been applied to improve soil quality [5,6] and to foster the activity and growth of microbial communities which are able to degrade hydrocarbons. These communities are often nutrient limited [7] and the addition of organic amendments palliates these deficiencies and support biodegradation of hydrocarbons [1,7,8].…”

“…Crude oil and related products are the major source of global energy and the risk for accidental spills during exploration, refining, industrial processes, and transport is an important concern of production companies and environmental authorities [1]. Linear and branched alkanes, cycloalkanes, and other mono-and poly-aromatic compounds comprise major fractions of hydrocarbon-containing products and have unintentionally been released to the environment causing the contamination of soil ecosystems and water bodies [2] with subsequent risks for humans and the environment.…”

Secondary successional trajectories of structural and catabolic bacterial communities in oil‐polluted soil planted with hybrid poplar

“…) for EDO and at 95% amino acid sequence similarity (in line with Wallisch et al . ) for AlkB in mothur . For both the catabolic genes, relative abundance of OTUs was calculated to normalize the number of sequences per sample.…”

“…A distance matrix of amino acid sequences was created with the protdist method in PHYLIP. OTUs were defined at 90% amino acid sequence similarity (according to Sipil€ a et al 2008) for EDO and at 95% amino acid sequence similarity (in line withWallisch et al 2014) for AlkB in MOTHUR. For both the catabolic genes, relative abundance of OTUs was calculated to normalize the number of sequences per sample.Table S2(Supporting information) lists the numbers of sequences which passed the different quality screening steps for the three pyrosequencing data sets.…”